The Department of Botany and Microbiology was established in 1995, and its foundation was contributed by a group of experienced and well-reputed faculty members. Notably, among the founding faculty members were Dr. Lotfy Mohsen (Faculty of Science, Aswan, formerly Assiut University) and Dr. Mohamed Soliman (Faculty of Science, Qena, formerly Assiut University). From the support staff, the contributors included Jihan Zaghloul (Faculty of Home Economics, formerly Helwan University), Rania Abu Hadeed, Entissar Nassar, Nermine El-Samri, Samah Ghanem, and Olfat Moatamed. Subsequently, a distinguished group of faculty members joined the department from the universities of Zagazig, Menoufia, Kafr El-Sheikh, and Tanta.

The department includes several sections such as Botany, Microbiology, Botany and Chemistry, as well as Microbiology and Biochemistry. The Biochemistry program, in particular, is unique to the college and has been offered since that time due to its significant applied importance in serving the community. Thus, the department combines both academic and applied specializations in essential scientific fields.

The Department of Botany and Microbiology has several collaborations with specialized scientific and research institutions, including the National Research Center, the Agricultural Research Center, the Drug Control Authority, Radiation Technology, the Desert Research Center, and the National Cancer Institute, among other scientific bodies in the Arab Republic of Egypt.

The Department of Botany and Microbiology is considered one of the prominent pillars of the Faculty of Science at Helwan University, distinguished by its reputable standing among botany and microbiology departments in various science faculties across Egyptian universities. The department boasts an elite group of faculty members whose expertise positively impacts the exceptional quality of graduates.

In addition to its well-equipped research laboratories, the department also houses the Botanical Herbarium, which contains a vast collection of classified and identified plant samples. The department is also renowned for its specialization in plant fossils, focusing on the study of plant remnants in archaeological excavations, as well as its specializations in biotechnology, tissue culture, and genetic engineering. This has facilitated the graduation of hundreds of students in postgraduate studies, obtaining master's and doctoral degrees.

Due to the notable participation of some faculty members from the Department of Botany and Microbiology in acquiring various academic, research, and applied projects at the university and national levels, and their active roles in scientific, research, and academic committees nationally — along with their significant contributions to accreditation and quality assurance committees nationally — these experiences have positively impacted the department. This was reflected in the accreditation of the Faculty of Science at Helwan University in 2018. Consequently, these efforts have enhanced the scientific capabilities of the department’s graduates in both undergraduate and postgraduate studies, enabling them to secure distinguished positions locally, regionally, and internationally, with many faculty members also being recruited by educational and research institutions abroad.